Make checking for for migrated tools when starting the Galaxy server a config setting that defaults to True. This setting should generally be False only for development Galaxy environments that are often set up from scratch (with new db, etc) and migrated tools are not needed in the Galaxy tool panel. In those cases where this setting is False, starting a fresh Galaxy instance (with no checking for migrated tools) will be much faster.

lib/galaxy/app.py

@@ -40,7 +40,8 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
 
         # Setup the database engine and ORM
         config_file = kwargs.get( 'global_conf', {} ).get( '__file__', None )
-        self._configure_models( check_migrate_databases=True, check_migrate_tools=True, config_file=config_file )
+        check_migrate_tools = self.config.check_migrate_tools
+        self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file )
 
         # Manage installed tool shed repositories.
         from tool_shed.galaxy_install import installed_repository_manager

lib/galaxy/config.py

@@ -4,8 +4,12 @@ Universe configuration builder.
 # absolute_import needed for tool_shed package.
 from __future__ import absolute_import
 
-import sys, os, tempfile, re
-import logging, logging.config
+import os
+import re
+import sys
+import tempfile
+import logging
+import logging.config
 import ConfigParser
 from datetime import timedelta
 from galaxy.web.formatting import expand_pretty_datetime_format
@@ -23,11 +27,14 @@ def resolve_path( path, root ):
         path = os.path.join( root, path )
     return path
 
+
 class ConfigurationError( Exception ):
     pass
 
+
 class Configuration( object ):
     deprecated_options = ( 'database_file', )
+
     def __init__( self, **kwargs ):
         self.config_dict = kwargs
         self.root = kwargs.get( 'root_dir', '.' )
@@ -87,6 +94,9 @@ class Configuration( object ):
         self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True )
 
         self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ]
+        # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have
+        # been migrated from the Galaxy code distribution to the Tool Shed.
+        self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) )
         self.shed_tool_data_path = kwargs.get( "shed_tool_data_path", None )
         if self.shed_tool_data_path:
             self.shed_tool_data_path = resolve_path( self.shed_tool_data_path, self.root )
@@ -397,13 +407,16 @@ class Configuration( object ):
             return rval
         except ConfigParser.NoSectionError:
             return {}
+
     def get( self, key, default ):
         return self.config_dict.get( key, default )
+
     def get_bool( self, key, default ):
         if key in self.config_dict:
             return string_as_bool( self.config_dict[key] )
         else:
             return default
+
     def check( self ):
         paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ]
         # Check that required directories exist
@@ -488,7 +501,6 @@ def get_database_engine_options( kwargs, model_prefix='' ):
             rval[ key  ] = value
     return rval
 
-
 def configure_logging( config ):
     """
     Allow some basic logging configuration to be read from ini file.

universe_wsgi.ini.sample

@@ -136,6 +136,13 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # Tools can be locally developed or installed from Galaxy tool sheds.
 #tool_config_file = tool_conf.xml,shed_tool_conf.xml
 
+# Enable / disable checking if any tools defined in the above non-shed tool_config_files
+# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool
+# Shed.  This setting should generally be set to False only for development Galaxy environments
+# that are often rebuilt from scratch where migrated tools do not need to be available in the
+# Galaxy tool panel.  If the following setting remains commented, the default setting will be True.
+#check_migrate_tools = True
+
 # Default path to the directory containing the tools defined in tool_conf.xml.
 # Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
 #tool_path = tools